This case has already been discussed on
@Riku 's FBI manual installation post.
It's caused by either you auto-downloaded the update nag or you Gateway-Downgraded your 3DS.
Both of them make FBI injection misjudge the TMD version.
You can't manually use the correct version since FBI injection refuses to accept the version not judged by itself.
Update emuNAND before injecting FBI is the best choice.
But if you are unable to update emuNAND, or you want to inject FBI to SysNAND, look at the following:
For update nag DLed 4.X, you should use Recovery Mode to clean up the update nag before injecting FBI.
For GW-DG 4.X, you have to manually inject FBI or restore undowngraded SysNAND before injecting FBI.